Martin J. O'Connor

95 papers B 7C 1Misc 24Journal 27Unranked 36

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Author Once, Publish Everywhere: Portable Metadata Authoring with the CEDAR Embeddable Editor. Data Sci. J. Martin J. O'Connor, Marcos Martínez Romero, Attila L. Egyedi, Mete Ugur Akdogan, Michael Dorf, Mark A. Musen
2026	J	`jnl`	Knowledge Engineering for Open Science: Building and Deploying Knowledge Bases for Metadata Standards. AI Mag. Mark A. Musen, Martin J. O'Connor, Josef Hardi, Marcos Martínez Romero
2025	J	`jnl`	Author Once, Publish Everywhere: Portable Metadata Authoring with the CEDAR Embeddable Editor. CoRR Martin J. O'Connor, Marcos Martínez Romero, Attila L. Egyedi, Mete Ugur Akdogan, Michael Dorf, Mark A. Musen
2025	J	`jnl`	Knowledge engineering for open science: Building and deploying knowledge bases for metadata standards. CoRR Mark A. Musen, Martin J. O'Connor, Josef Hardi, Marcos Martínez Romero
2025	J	`jnl`	RADx Data Hub: A Cloud Platform for FAIR, Harmonized COVID-19 Data. CoRR Marcos Martínez Romero, Matthew Horridge, Nilesh Mistry, Aubrie Weyhmiller, Jimmy K. Yu, Alissa Fujimoto, Aria Henry, Martin J. O'Connor, Ashley Sier, Stephanie Suber, Mete Ugur Akdogan, Yan Cao, Somu Valliappan, Joanna O. Mieczkowska, RADx Data Hub team, Ashok Krishnamurthy, Michael A. Keller, Mark A. Musen
2024	J	`jnl`	Ensuring Adherence to Standards in Experiment-Related Metadata Entered Via Spreadsheets. CoRR Martin J. O'Connor, Josef Hardi, Marcos Martínez Romero, Sowmya Somasundaram, Brendan Honick, Stephen A. Fisher, Ajay Pillai, Mark A. Musen
2023	J	`jnl`	A Comprehensive Approach to Ensuring Quality in Spreadsheet-Based Metadata. CoRR Martin J. O'Connor, Marcos Martínez Romero, Mete Ugur Akdogan, Josef Hardi, Mark A. Musen
2022	J	`jnl`	Modeling community standards for metadata as templates makes data FAIR. CoRR Mark A. Musen, Martin J. O'Connor, Erik Schultes, Marcos Martínez Romero, Josef Hardi, John B. Graybeal
2019	J	`jnl`	The CEDAR Workbench: An Ontology-Assisted Environment for Authoring Metadata that Describe Scientific Experiments. CoRR Rafael S. Gonçalves, Martin J. O'Connor, Marcos Martínez Romero, Attila L. Egyedi, Debra Willrett, John B. Graybeal, Mark A. Musen
2019	Misc	`conf`	Unleashing the value of Common Data Elements through the CEDAR Workbench. AMIA Martin J. O'Connor, Denise B. Warzel, Marcos Martínez Romero, Josef Hardi, Debra Willrett, Aras Efekhari, John B. Graybeal, Mark A. Musen
2019	J	`jnl`	Using association rule mining and ontologies to generate metadata recommendations from multiple biomedical databases. Database J. Biol. Databases Curation Marcos Martínez Romero, Martin J. O'Connor, Attila L. Egyedi, Debra Willrett, Josef Hardi, John B. Graybeal, Mark A. Musen
2019	J	`jnl`	Using association rule mining and ontologies to generate metadata recommendations from multiple biomedical databases. CoRR Marcos Martínez Romero, Martin J. O'Connor, Attila L. Egyedi, Debra Willrett, Josef Hardi, John B. Graybeal, Mark A. Musen
2018	J	`jnl`	CEDAR OnDemand: a browser extension to generate ontology-based scientific metadata. BMC Bioinform. Syed Ahmad Chan Bukhari, Marcos Martínez Romero, Martin J. O'Connor, Attila L. Egyedi, Debra Willrett, John B. Graybeal, Mark A. Musen, Kei-Hoi Cheung, Steven H. Kleinstein
2018	—	`conf`	Using Ontologies to Drive the Creation of High-Quality Metadata in CEDAR. ISWC (P&D/Industry/BlueSky) Rafael S. Gonçalves, Csongor I. Nyulas, Marcos Martínez Romero, Martin J. O'Connor, John B. Graybeal, Mark A. Musen
2018	—	`conf`	Using semantic technologies to enhance metadata submissions to public repositories in biomedicine. SWAT4LS Attila L. Egyedi, Martin J. O'Connor, Marcos Martínez Romero, Debra Willrett, Josef Hardi, John B. Graybeal, Mark A. Musen
2017	—	`conf`	Embracing Semantic Technology for Better Metadata Authoring in Biomedicine. SWAT4LS Attila L. Egyedi, Martin J. O'Connor, Marcos Martínez Romero, Debra Willrett, Josef Hardi, John B. Graybeal, Mark A. Musen
2017	Misc	`conf`	Fast and Accurate Metadata Authoring Using Ontology-Based Recommendations. AMIA Marcos Martínez Romero, Martin J. O'Connor, Ravi D. Shankar, Maryam Panahiazar, Debra Willrett, Attila Levente Egyedi, Olivier Gevaert, John B. Graybeal, Mark A. Musen
2017	—	`conf`	Metadata in the BioSample Online Repository are Impaired by Numerous Anomalies. SemSci@ISWC Rafael S. Gonçalves, Martin J. O'Connor, Marcos Martínez Romero, John B. Graybeal, Mark A. Musen
2017	J	`jnl`	Metadata in the BioSample Online Repository are Impaired by Numerous Anomalies. CoRR Rafael S. Gonçalves, Martin J. O'Connor, Marcos Martínez Romero, John B. Graybeal, Mark A. Musen
2017	J	`jnl`	NCBO Ontology Recommender 2.0: an enhanced approach for biomedical ontology recommendation. J. Biomed. Semant. Marcos Martínez Romero, Clément Jonquet, Martin J. O'Connor, John B. Graybeal, Alejandro Pazos, Mark A. Musen
2017	—	`conf`	Supporting Ontology-Based Standardization of Biomedical Metadata in the CEDAR Workbench. ICBO Marcos Martínez Romero, Martin J. O'Connor, Michael Dorf, Jennifer Vendetti, Debra Willrett, Attila L. Egyedi, John B. Graybeal, Mark A. Musen
2017	—	`conf`	The CEDAR Workbench: An Ontology-Assisted Environment for Authoring Metadata that Describe Scientific Experiments. ISWC (2) Rafael S. Gonçalves, Martin J. O'Connor, Marcos Martínez Romero, Attila L. Egyedi, Debra Willrett, John B. Graybeal, Mark A. Musen
2016	B	`conf`	An Open Repository Model for Acquiring Knowledge About Scientific Experiments. EKAW Martin J. O'Connor, Marcos Martínez Romero, Attila L. Egyedi, Debra Willrett, John B. Graybeal, Mark A. Musen
2016	Misc	`conf`	CEDAR: Better Data Sharing Through the Authoring of Better Metadata. AMIA Mark A. Musen, Martin J. O'Connor, Marcos Martínez Romero, Attila Levente Egyedi, Debra Willrett, John B. Graybeal
2016	J	`jnl`	NCBO Ontology Recommender 2.0: An Enhanced Approach for Biomedical Ontology Recommendation. CoRR Marcos Martínez Romero, Clément Jonquet, Martin J. O'Connor, John B. Graybeal, Alejandro Pazos, Mark A. Musen
2015	J	`jnl`	The center for expanded data annotation and retrieval. J. Am. Medical Informatics Assoc. Mark A. Musen, Carol A. Bean, Kei-Hoi Cheung, Michel Dumontier, Kim A. Durante, Olivier Gevaert, Alejandra N. González-Beltrán, Purvesh Khatri, Steven H. Kleinstein, Martin J. O'Connor, Yannick Pouliot, Philippe Rocca-Serra, Susanna-Assunta Sansone, Jeffrey A. Wiser
2014	J	`jnl`	Clustering rule bases using ontology-based similarity measures. J. Web Semant. Saeed Hassanpour, Martin J. O'Connor, Amar K. Das
2013	J	`jnl`	A semantic-based method for extracting concept definitions from scientific publications: evaluation in the autism phenotype domain. J. Biomed. Semant. Saeed Hassanpour, Martin J. O'Connor, Amar K. Das
2012	—	`conf`	A Pair of OWL 2 RL Reasoners. OWLED Martin J. O'Connor, Amar K. Das
2012	J	`jnl`	Adaptive System for Collaborative Online Laboratories. IEEE Intell. Syst. Christophe Gravier, Jacques Fayolle, Jérémy Lardon, Martin J. O'Connor
2012	—	`conf`	SWRL Rule Editor - A Web Application as Rich as Desktop Business Rule Editors. ICEIS (2) João Paulo Orlando, Adriano Rivolli, Saeed Hassanpour, Martin J. O'Connor, Amar K. Das, Dilvan A. Moreira
2011	—	`conf`	A Framework for the Automatic Extraction of Rules from Online Text. RuleML Europe Saeed Hassanpour, Martin J. O'Connor, Amar K. Das
2011	B	`conf`	A Rule-Based Method for Specifying and Querying Temporal Abstractions. AIME Martin J. O'Connor, Genaro Hernández, Amar K. Das
2011	B	`conf`	Acquiring OWL ontologies from XML documents. K-CAP Martin J. O'Connor, Amar K. Das
2011	J	`jnl`	Overcoming the ontology enrichment bottleneck with Quick Term Templates. Appl. Ontology Philippe Rocca-Serra, Alan Ruttenberg, Martin J. O'Connor, Patricia L. Whetzel, Daniel Schober, Jay Greenbaum, Mélanie Courtot, Ryan Remy Brinkman, Susanna-Assunta Sansone, Richard H. Scheuermann, Bjoern Peters
2011	—	`conf`	SWEETInfo: a Web-Based System for Visualizing and Querying Temporal Data. RuleML America (2) Martin J. O'Connor, Amanda Richards, Susana B. Martins, Mike Bingen, Samson W. Tu, Amar K. Das
2011	—	`conf`	SWRL-F: a fuzzy logic extension of the semantic web rule language. WIMS Tomasz Wiktor Wlodarczyk, Chunming Rong, Martin J. O'Connor, Mark A. Musen
2011	B	`conf`	Web-Based Querying and Temporal Visualization of Longitudinal Clinical Data. AIME Amanda Richards, Martin J. O'Connor, Susana B. Martins, Michael Uehara-Bingen, Samson W. Tu, Amar K. Das
2011	C	`conf`	Web-based Exploration of Temporal Data in Biomedicine. WEBIST Martin J. O'Connor, Mike Bingen, Amanda Richards, Samson W. Tu, Amar K. Das
2010	—	`conf`	A Lightweight Model for Representing and Reasoning with Temporal Information in Biomedical Ontologies. HEALTHINF Martin J. O'Connor, Amar K. Das
2010	—	`conf`	A Method for Representing and Querying Temporal Information in OWL. BIOSTEC (Selected Papers) Martin J. O'Connor, Amar K. Das
2010	—	`conf`	A Software Tool for Visualizing, Managing and Eliciting SWRL Rules. ESWC (2) Saeed Hassanpour, Martin J. O'Connor, Amar K. Das
2010	—	`conf`	M OWLED Martin J. O'Connor, Christian Halaschek-Wiener, Mark A. Musen
2010	—	`conf`	Mapping Master: A Flexible Approach for Mapping Spreadsheets to OWL. ISWC (2) Martin J. O'Connor, Christian Halaschek-Wiener, Mark A. Musen
2010	—	`conf`	SWRL-F - A Fuzzy Logic Extension of the Semantic Web Rule Language. URSW Tomasz Wiktor Wlodarczyk, Martin J. O'Connor, Chunming Rong, Mark A. Musen
2010	—	`conf`	Semantic Reasoning with XML-based Biomedical Information Models. MedInfo Martin J. O'Connor, Amar K. Das
2010	—	`conf`	Visualizing Logical Dependencies in SWRL Rule Bases. RuleML Saeed Hassanpour, Martin J. O'Connor, Amar K. Das
2009	Misc	`conf`	A Bayesian Network Model for Analysis of Detection Performance in Surveillance Systems. AMIA Masoumeh T. Izadi, David L. Buckeridge, Anna Okhmatovskaia, Samson W. Tu, Martin J. O'Connor, Csongor Nyulas, Mark A. Musen
2009	—	`conf`	A Rule Management and Elicitation Tool for SWRL Rule Bases. RuleML Challenge Saeed Hassanpour, Martin J. O'Connor, Amar K. Das
2009	—	`conf`	Axiomé: A Tool for the Elicitation and Management of SWRL Rules. OWLED Saeed Hassanpour, Martin J. O'Connor, Amar K. Das
2009	—	`conf`	Exploration of SWRL Rule Bases through Visualization, Paraphrasing, and Categorization of Rules. RuleML Saeed Hassanpour, Martin J. O'Connor, Amar K. Das
2009	J	`jnl`	Knowledge-data integration for temporal reasoning in a clinical trial system. Int. J. Medical Informatics Martin J. O'Connor, Ravi D. Shankar, David B. Parrish, Amar K. Das
2009	—	`conf`	SQWRL: A Query Language for OWL. OWLED Martin J. O'Connor, Amar K. Das
2009	Misc	`conf`	Semantic Reasoning with Image Annotations for Tumor Assessment. AMIA Mia A. Levy, Martin J. O'Connor, Daniel L. Rubin
2009	J	`jnl`	Software-engineering challenges of building and deploying reusable problem solvers. Artif. Intell. Eng. Des. Anal. Manuf. Martin J. O'Connor, Csongor Nyulas, Samson W. Tu, David L. Buckeridge, Anna Okhmatovskaia, Mark A. Musen
2008	—	`conf`	An Ontological Approach to Representing and Reasoning with Temporal Constraints in Clinical Trial Protocols. HEALTHINF (1) Ravi D. Shankar, Susana B. Martins, Martin J. O'Connor, Amar K. Das
2008	—	`conf`	An Ontology-Driven Framework for Deploying JADE Agent Systems. IAT Csongor Nyulas, Martin J. O'Connor, Samson W. Tu, David L. Buckeridge, Anna Okhmatovskaia, Mark A. Musen
2008	—	`conf`	Developing a Web-Based Application using OWL and SWRL. AAAI Spring Symposium: AI Meets Business Rules and Process Management Martin J. O'Connor, Ravi D. Shankar, Csongor Nyulas, Samson W. Tu, Amar K. Das
2008	J	`jnl`	Model Formulation: Understanding Detection Performance in Public Health Surveillance: Modeling Aberrancy-detection Algorithms. J. Am. Medical Informatics Assoc. David L. Buckeridge, Anna Okhmatovskaia, Samson W. Tu, Martin J. O'Connor, Csongor Nyulas, Mark A. Musen
2008	Misc	`conf`	Predicting Outbreak Detection in Public Health Surveillance: Quantitative Analysis to Enable Evidence-Based Method Selection. AMIA David L. Buckeridge, Anna Okhmatovskaia, Samson W. Tu, Martin J. O'Connor, Csongor Nyulas, Mark A. Musen
2008	—	`conf`	Representing and Reasoning with Temporal Constraints in Clinical Trials Using Semantic Technologies. BIOSTEC (Selected Papers) Ravi D. Shankar, Susana B. Martins, Martin J. O'Connor, David B. Parrish, Amar K. Das
2008	—	`conf`	Semantic Integration of Software Systems in Translational Clinical Trials. AAAI Spring Symposium: Semantic Scientific Knowledge Integration Ravi D. Shankar, Martin J. O'Connor, David B. Parrish, Amar K. Das
2008	—	`conf`	The SWRLAPI: A Development Environment for Working with SWRL Rules. OWLED Martin J. O'Connor, Ravi D. Shankar, Mark A. Musen, Amar K. Das, Csongor Nyulas
2008	Misc	`conf`	Using an Integrated Ontology and Information Model for Querying and Reasoning about Phenotypes: The Case of Autism. AMIA Samson W. Tu, Lakshika Tennakoon, Martin J. O'Connor, Ravi D. Shankar, Amar K. Das
2007	Misc	`conf`	An Ontology-Driven Method for Hierarchical Mining of Temporal Patterns: Application to HIV Drug Resistance Research. AMIA Rashmi Raj, Martin J. O'Connor, Amar K. Das
2007	Misc	`conf`	An Ontology-based Architecture for Integration of Clinical Trials Management Applications. AMIA Ravi D. Shankar, Susana B. Martins, Martin J. O'Connor, David B. Parrish, Amar K. Das
2007	—	`conf`	Efficiently Querying Relational Databases Using OWL and SWRL. RR Martin J. O'Connor, Ravi D. Shankar, Samson W. Tu, Csongor Nyulas, Amar K. Das, Mark A. Musen
2007	—	`conf`	Knowledge-Level Querying of Temporal Patterns in Clinical Research Systems. MedInfo Martin J. O'Connor, Ravi D. Shankar, David B. Parrish, Amar K. Das
2007	—	`conf`	Querying the Semantic Web with SWRL. RuleML Martin J. O'Connor, Samson W. Tu, Csongor Nyulas, Amar K. Das, Mark A. Musen
2007	B	`conf`	Using Semantic Web Technologies for Knowledge-Driven Querying of Biomedical Data. AIME Martin J. O'Connor, Ravi D. Shankar, Samson W. Tu, Csongor Nyulas, Dave Parrish, Mark A. Musen, Amar K. Das
2006	Misc	`conf`	A Dynamic Distributed Architecture for Temporal Data Abstraction. AMIA Vijay P. Chauhan, Martin J. O'Connor, Amar K. Das
2006	B	`conf`	An Ontology-Driven Mediator for Querying Time-Oriented Biomedical Data. CBMS Martin J. O'Connor, Ravi D. Shankar, Amar K. Das
2006	—	`conf`	Epoch: an ontological framework to support clinical trials management. HIKM Ravi D. Shankar, Susana B. Martins, Martin J. O'Connor, David B. Parrish, Amar K. Das
2006	B	`conf`	Knowledge-Based System for Managing Complex Clinical Trials. CBMS Ravi D. Shankar, Susana B. Martins, Martin J. O'Connor, David B. Parrish, Amar K. Das
2006	Misc	`conf`	Ontology-Driven Mapping of Temporal Data in Biomedical Databases. AMIA Preetha S. Narayanan, Martin J. O'Connor, Amar K. Das
2006	Misc	`conf`	Towards Semantic Interoperability in a Clinical Trials Management System. ISWC Ravi D. Shankar, Susana B. Martins, Martin J. O'Connor, David B. Parrish, Amar K. Das
2005	—	`conf`	Computational Method for Temporal Pattern Discovery in Biomedical Genomic Databases. CSB Mohammed I. Rafiq, Martin J. O'Connor, Amar K. Das
2005	—	`conf`	Knowledge-Based Syndromic Surveillance for Bioterrorism. AAAI Spring Symposium: AI Technologies for Homeland Security Mark A. Musen, Monica Crubézy, Martin J. O'Connor, David L. Buckeridge
2005	J	`jnl`	Ontology-Centered Syndromic Surveillance for Bioterrorism. IEEE Intell. Syst. Monica Crubézy, Martin J. O'Connor, David L. Buckeridge, Zachary Pincus, Mark A. Musen
2005	Misc	`conf`	Supporting Rule System Interoperability on the Semantic Web with SWRL. ISWC Martin J. O'Connor, Holger Knublauch, Samson W. Tu, Benjamin N. Grosof, Mike Dean, William E. Grosso, Mark A. Musen
2004	Misc	`conf`	A Knowledge-Based Framework for Deploying Surveillance Problem Solvers. IKE David L. Buckeridge, Martin J. O'Connor, Haobo Xu, Mark A. Musen
2004	J	`jnl`	Application of Information Technology: Translating Research into Practice: Organizational Issues in Implementing Automated Decision Support for Hypertension in Three Medical Centers. J. Am. Medical Informatics Assoc. Mary K. Goldstein, Robert W. Coleman, Samson W. Tu, Ravi D. Shankar, Martin J. O'Connor, Mark A. Musen, Susana B. Martins, Philip W. Lavori, Michael G. Shlipak, Eugene Oddone, Aneel A. Advani, Parisa Gholami, Brian B. Hoffman
2003	Misc	`conf`	BioSTORM: A System for Automated Surveillance of Diverse Data Sources. AMIA Martin J. O'Connor, David L. Buckeridge, Michael Choy, Monica Crubézy, Zachary Pincus, Mark A. Musen
2002	Misc	`conf`	Knowledge-based bioterrorism surveillance. AMIA David L. Buckeridge, Justin Graham, Martin J. O'Connor, Michael Choy, Samson W. Tu, Mark A. Musen
2002	J	`jnl`	Patient Safety in Guideline-Based Decision Support for Hypertension Management: ATHENA DSS. J. Am. Medical Informatics Assoc. Mary K. Goldstein, Brian B. Hoffman, Robert W. Coleman, Samson W. Tu, Ravi D. Shankar, Martin J. O'Connor, Susana B. Martins, Aneel A. Advani, Mark A. Musen
2002	Misc	`conf`	The Chronus II temporal database mediator. AMIA Martin J. O'Connor, Samson W. Tu, Mark A. Musen
2001	Misc	`conf`	A Client-Server Framework for Deploying a Decision-support System in a Resource-constrained Environment. AMIA Martin J. O'Connor, Ravi D. Shankar, Samson W. Tu, Aneel A. Advani, Mary K. Goldstein, Robert W. Coleman, Mark A. Musen
2001	Misc	`conf`	Patient safety in guideline-based decision support for hypertension management: ATHENA DSS. AMIA Mary K. Goldstein, Brian B. Hoffman, Robert W. Coleman, Samson W. Tu, Ravi D. Shankar, Martin J. O'Connor, Susana B. Martins, Aneel A. Advani, Mark A. Musen
2001	—	`conf`	RASTA: A Distributed Temporal Abstraction System to Facilitate Knowledge-Driven Monitoring of Clinical Databases. MedInfo Martin J. O'Connor, William E. Grosso, Samson W. Tu, Mark A. Musen
2000	Misc	`conf`	Implementing clinical practice guidelines while taking account of changing evidence: ATHENA DSS, an easily modifiable decision-support system for managing hypertension in primary care. AMIA Mary K. Goldstein, Brian B. Hoffman, Robert W. Coleman, Mark A. Musen, Samson W. Tu, Aneel A. Advani, Ravi D. Shankar, Martin J. O'Connor
2000	Misc	`conf`	Representation of temporal indeterminacy in clinical databases. AMIA Martin J. O'Connor, Samson W. Tu, Mark A. Musen
1999	Misc	`conf`	Applying temporal joins to clinical databases. AMIA Martin J. O'Connor, Samson W. Tu, Mark A. Musen
1999	Misc	`conf`	EON 2.0: Enhanced Middleware for Automation of Protocol-Directed Therapy. AMIA Mark A. Musen, Samson W. Tu, Ravi D. Shankar, Martin J. O'Connor, Aneel A. Advani
1999	Misc	`conf`	Integrating a modern knowledge-based system architecture with a legacy VA database: the ATHENA and EON projects at Stanford. AMIA Aneel A. Advani, Samson W. Tu, Martin J. O'Connor, Robert W. Coleman, Mary K. Goldstein, Mark A. Musen
1994	J	`jnl`	Micro-kernel support for migration. Distributed Syst. Eng. Martin J. O'Connor, Brendan Tangney, Vinny Cahill, Neville Harris